3D Model of replicating chromatin: Yeast_full_genome

Source code for the simulations described in  Dario D’Asaro et al. “Genome-wide modeling of DNA replication in space and time confirms the emergence of replication specific patterns in vivo in eukaryotes”.

The version of the code used in the article is  a branch named Yeast_full_genome of the git repository https://github.com/physical-biology-of-chromatin/LatticePoly. The code is based on a Kinetic Monte Carlo algorithm to model on lattice chromatin structure and dynamics. The version here deposited additionally includes (1) Explicit synthesis of sister chromatids due to DNA replication. (2) Large scale Rabl-organization of budding yeast nucleus.